Subproject #1 Selective Plane Illumination Microscopy for nematode neurodevelopment and minimally invasive in vivo imaging Selective plane illumination microscopy (SPIM (1)) is a technique whereby a sample is illuminated with a thin plane of light from the side, so that fluorescence detection occurs in a direction perpendicular to excitation. Such an experimental geometry has major advantages over conventional 3D microscopy techniques, such as confocal or 2 photon microscopy. First, acquisition speed is greatly increased relative to point-scanning methods, as the entire imaging plane is detected simultaneously. Second, excitation is confined to the focal plane, so each pixel is imaged only once during each volumetric acquisition. This drastically reduces light exposure and results in far lower photobleaching and photodamage than is possible with conventional imaging techniques. These advantages have been applied to studying whole-animal (zebrafish, drosophila) embryogenesis, and to the measurement of calcium transients in tissue slices. We are using our implementation of SPIM to construct the first atlas of neuronal positions and migrations in the developing nematode C. Elegans, in collaboration with extramural researchers Daniel Colon-Ramos (Yale University), Zhirong Bao (Memorial Sloan-Kettering Cancer Center), and William Mohler (University of Connecticut). Due to the greatly reduced light dosage, we imaged nematode embryogenesis at 30x the speed of the best available competing technology (spinning disk confocal microscopy), with equivalent signal-to-noise ratio. This advance enabled the visualization of fast neurodevelopmental events in vivo (2). We have also constructed a second generation SPIM instrument, where illumination and detection is conducted along two perpendicular views (dual-view inverted selective plane illumination microscopy, diSPIM). The advantage of the diSPIM is that axial resolution is significantly increased by merging the results obtained from each view. This setup enables isotropic imaging with 330 nm, more than quadrupling axial resolution compared to our previous instrument. We can maintain this high spatial resolution while also operating the microscope at high frame rates, up to 200 Hz in 2D and 2 Hz in 3D (for a 50 plane volume). The microscope enables high resolution, 4D imaging with minimal photobleaching and photodamage in cells and small embryos (3, 4). We have now developed methods that further increase the resolution and sensitivity of diSPIM, by adding additional specimen views to the microscope (5). In combination with hardware improvements, we have also collaborated with computer scientists at the NIH to develop new software tools, that enable the computational 'untwisting' of embryo data acquired with our diSPIM. This untwisting software has enabled us to track the relative orientations and positions of cells within the twitching embryo, thus enabling a systems-biology level view of the entire elongating worm embryo (6). An closely-related subproject is the development of software that renders, displays and disseminates the growing 4D atlas of cell positions that we are obtaining with our microscope (7). Finally, an emerging focus in the lab is the tracking of behavior and calcium flux (8) as the embryo develops. Subproject #2 Increasing the speed and depth penetration of structured illumination microscopy Structured illumination microscopy (SIM) is a super-resolution technique (9) that offers modest resolution improvement (2x better than the diffraction limit), but is readily compatible with live samples due to its low excitation intensities. SIM, while commercially available, is expensive and remains the province of relatively few labs. Furthermore, commercial SIM systems are limited to samples with thickness < 10 microns, as they do not physically reject background light. Together with Chris Combs (NHLBI), we developed a multifocal version of SIM (MSIM) that uses the confocal effect to image samples > 50 micronsfrom the coverslip surface while maintaining resolution-doubling capability (10). We have also developed an MSIM implementation that improves the speed of acquisition 100-fold, by performing most of the computational processing operations entirely in hardware (instant SIM, (11). We have also developed a point-scanning, multiphoton version of the instant SIM that better depth penetration (12, 13) than the single-photon implementation, and continue to work on further pushing the depth penetrance by integrating adaptive optics into the microscope (14). We actively seek collaborators in order to apply these systems to biology. (1) Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J. & Stelzer, E. H. K. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305, 1007-9 (2004). (2) Wu, Y. et al. Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 108, 17708-17713 (2011). (3) Wu, Y., Wawrzusin, P., Senseney, J., Fischer, R.S., Christensen, R., Santella, A., York, A.G., Winter, P.W., Waterman, C.M., Bao, Z., Colon-Ramos, D., McAuliffe, M., Shroff, H. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat. Biotechnol. 31, 1032-8 (2013). (4) Kumar, A., Wu, Y., Christensen, R., Chandris, P., Gandler, W., McCreedy, E., Bokinsky, A., Colon-Ramos, D.A., Bao, Z., McAuliffe, M., Rondeau, G., Shroff, H. Assembly and use of dual-view inverted plane illumination microscope for rapid, spatially isotropic four-dimensional imaging. Nature Protocols 9(11):2555-73 (2014). (5) Wu, Y., Chandris, P., ,Winter, P.W., Kim, E.Y., Jaumouille, V., Kumar, A., Guo, M., Leung, J.M., Smith, C., Rey-Suarez, I., Liu, H., Waterman, C.M., Ramamurthi, K.S., LaRiviere, P., Shroff, H. Simultaneous multi-view capture and fusion improves spatial resolution in wide-field and light-sheet microscopy. Optica, 8 897-910 (2016). (6) Christensen, R., Bokinsky, A., Santella, A., Wu, Y., Marquina-Solis, J., Guo, M., Kovacevik, I., Kumar, A., Winter, P.W., Tashakkori, N., McCreedy, E., Liu, H., McAuliffe, M., Mohler, W., Colon-Ramos, D.A., Bao, Z., Shroff, H. Untwisting the Caenorhabditis elegans embryo. eLife 10070 (2015). (7) Santella A., et al. WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. BMC Bioinformatics. 16:189 (2015). (8) Ardiel E., et al. Visualizing Calcium Flux in Freely Moving Nematode Embryos. Biophys J. 112(9):1975-1983. (9) Gustafsson, M.G. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc. 198, 82-7 (2000). (10) York, A.G. et al. Resolution Doubling in Live, Multicellular Organisms via Multifocal Structured Illumination Microscopy. Nat. Methods 9, 749-754 (2012). (11) York, A.G., Chandris, P., Dalle Nogare, D., Head, J., Wawrzusin, P., Fischer, R.S., Chitnis, A., Shroff, H. Instant super-resolution imaging in live cells and embryos via analog image processing. Nat. Methods 10, 1122-6 (2013). (12) Winter, P., York, A.G., Dalle Nogare, D., Ingaramo, M., Christensen, R., Chitnis, A., Patterson, G.H., Shroff, H. Two-photon instant structured illumination microscopy improves the depth penetration of super-resolution imaging in thick scattering samples. Optica 1(3):181-191 (2014). (13) Winter PW, Chandris P, Fischer RS, Wu Y, Waterman CM, Shroff H. Incoherent structured illumination improves optical sectioning and contrast in multiphoton super-resolution microscopy. Opt Express. 23(4):5327-34 (2015). (14) Zheng, W., et al. Adaptive optics improves multiphoton super-resolution imaging. Nat. Methods Nat Methods. 2017, AOP